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FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 539MZ

Calculation Name: 5RS7-B-Xray89

Preferred Name:

Target Type:

Ligand Name: 1-{2-[(propan-2-yl)oxy]ethyl}-2-sulfanylidene-1,2,3,5-tetrahydro-4h-pyrrolo[3,2-d]pyrimidin-4-one

ligand 3-letter code: W4Y

PDB ID: 5RS7

Chain ID: B

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2021-09-27

Reference: T. Ohyama, K. Kamisaka, C. Watanabe, T. Honma et. al., FMO-based interaction energy analysis of SARS-Cov-2 related protein and ligand complexes, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHLSideSolv
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water Waters within average of the temperature factors of receptor.
Procedure Auto-FMO protocol ver. 1.20200406
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 206
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1785996.101399
FMO2-HF: Nuclear repulsion 1719613.856068
FMO2-HF: Total energy -66382.245331
FMO2-MP2: Total energy -66575.819388


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(B:1:SER )


Summations of interaction energy for fragment #1(B:1:SER )
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-1.6510.821-0.01-1.1-1.3620.005
Interaction energy analysis for fragmet #1(B:1:SER )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : 0.001
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3B3VAL 00.0420.0173.722-0.6091.863-0.010-1.100-1.3620.005
4B4ASN 0-0.005-0.0106.031-0.590-0.5900.0000.0000.0000.000
5B5SER 00.0080.0077.987-0.139-0.1390.0000.0000.0000.000
6B6PHE 0-0.023-0.01010.0650.0650.0650.0000.0000.0000.000
7B7SER 00.0310.00713.882-0.046-0.0460.0000.0000.0000.000
8B8GLY 00.0180.00615.7770.0500.0500.0000.0000.0000.000
9B9TYR 0-0.080-0.05916.6080.0300.0300.0000.0000.0000.000
10B10LEU 00.0180.02120.885-0.022-0.0220.0000.0000.0000.000
11B11LYS 10.8580.92723.7440.1910.1910.0000.0000.0000.000
12B12LEU 0-0.038-0.00724.9550.0070.0070.0000.0000.0000.000
13B13THR 00.035-0.00826.5820.0010.0010.0000.0000.0000.000
14B14ASP -1-0.871-0.94925.450-0.163-0.1630.0000.0000.0000.000
15B15ASN 0-0.036-0.01322.494-0.021-0.0210.0000.0000.0000.000
16B16VAL 00.0180.02122.3420.0090.0090.0000.0000.0000.000
17B17TYR 0-0.0020.00220.716-0.020-0.0200.0000.0000.0000.000
18B18ILE 00.0100.00822.7630.0200.0200.0000.0000.0000.000
19B19LYS 10.8430.90117.8140.0870.0870.0000.0000.0000.000
20B20ASN 0-0.043-0.01222.8540.0120.0120.0000.0000.0000.000
21B21ALA 00.006-0.01319.982-0.007-0.0070.0000.0000.0000.000
22B22ASP -1-0.810-0.88821.0390.0940.0940.0000.0000.0000.000
23B23ILE 00.0340.00318.7520.0030.0030.0000.0000.0000.000
24B24VAL 00.0190.01717.4590.0260.0260.0000.0000.0000.000
25B25GLU -1-0.813-0.89616.1740.1880.1880.0000.0000.0000.000
26B26GLU -1-0.775-0.85615.136-0.073-0.0730.0000.0000.0000.000
27B27ALA 0-0.0020.00013.410-0.010-0.0100.0000.0000.0000.000
28B28LYS 10.8400.90711.449-0.144-0.1440.0000.0000.0000.000
29B29LYS 10.7810.88710.4190.1380.1380.0000.0000.0000.000
30B30VAL 0-0.081-0.0379.575-0.072-0.0720.0000.0000.0000.000
31B31LYS 10.9801.0085.191-0.445-0.4450.0000.0000.0000.000
32B32PRO 00.0190.0258.0060.1430.1430.0000.0000.0000.000
33B33THR 00.0120.00010.2580.2380.2380.0000.0000.0000.000
34B34VAL 0-0.012-0.01310.9720.0310.0310.0000.0000.0000.000
35B35VAL 0-0.0080.00614.656-0.049-0.0490.0000.0000.0000.000
36B36VAL 0-0.006-0.00216.6540.0110.0110.0000.0000.0000.000
37B37ASN 00.003-0.03020.424-0.013-0.0130.0000.0000.0000.000
38B38ALA 0-0.0160.01622.841-0.009-0.0090.0000.0000.0000.000
39B39ALA 00.0350.03426.1000.0000.0000.0000.0000.0000.000
40B40ASN 00.019-0.00427.863-0.009-0.0090.0000.0000.0000.000
41B41VAL 00.0230.00730.5500.0080.0080.0000.0000.0000.000
42B42TYR 00.0400.01632.4860.0030.0030.0000.0000.0000.000
43B43LEU 0-0.034-0.00526.4340.0060.0060.0000.0000.0000.000
44B44LYS 10.8550.93328.978-0.100-0.1000.0000.0000.0000.000
45B45HIS 00.0060.00425.652-0.019-0.0190.0000.0000.0000.000
46B46GLY 00.0330.02528.4140.0030.0030.0000.0000.0000.000
47B47GLY 00.0220.00030.3250.0010.0010.0000.0000.0000.000
48B48GLY 00.0070.00029.0070.0040.0040.0000.0000.0000.000
49B49VAL 00.0620.02523.0530.0080.0080.0000.0000.0000.000
50B50ALA 00.0110.01924.1730.0150.0150.0000.0000.0000.000
51B51GLY 0-0.0080.01124.9950.0140.0140.0000.0000.0000.000
52B52ALA 0-0.035-0.02823.5200.0100.0100.0000.0000.0000.000
53B53LEU 00.0150.00018.7780.0160.0160.0000.0000.0000.000
54B54ASN 00.0650.02020.7580.0370.0370.0000.0000.0000.000
55B55LYS 10.9310.97222.775-0.107-0.1070.0000.0000.0000.000
56B56ALA 00.0110.02018.4730.0080.0080.0000.0000.0000.000
57B57THR 0-0.042-0.01517.8510.0260.0260.0000.0000.0000.000
58B58ASN 0-0.027-0.01819.682-0.009-0.0090.0000.0000.0000.000
59B59ASN 0-0.012-0.00622.775-0.011-0.0110.0000.0000.0000.000
60B60ALA 00.0500.03720.400-0.010-0.0100.0000.0000.0000.000
61B61MET 00.0350.03719.710-0.012-0.0120.0000.0000.0000.000
62B62GLN 0-0.042-0.03522.398-0.015-0.0150.0000.0000.0000.000
63B63VAL 0-0.0030.00725.356-0.010-0.0100.0000.0000.0000.000
64B64GLU -1-0.724-0.84320.5220.2800.2800.0000.0000.0000.000
65B65SER 0-0.027-0.02324.721-0.011-0.0110.0000.0000.0000.000
66B66ASP -1-0.819-0.89126.5480.1090.1090.0000.0000.0000.000
67B67ASP -1-0.913-0.94327.3480.1480.1480.0000.0000.0000.000
68B68TYR 00.0540.01226.049-0.008-0.0080.0000.0000.0000.000
69B69ILE 0-0.039-0.01928.319-0.011-0.0110.0000.0000.0000.000
70B70ALA 0-0.029-0.00131.651-0.009-0.0090.0000.0000.0000.000
71B71THR 0-0.042-0.00930.162-0.007-0.0070.0000.0000.0000.000
72B72ASN 0-0.085-0.05428.652-0.009-0.0090.0000.0000.0000.000
73B73GLY 0-0.026-0.00232.422-0.008-0.0080.0000.0000.0000.000
74B74PRO 0-0.054-0.03032.6370.0060.0060.0000.0000.0000.000
75B75LEU 0-0.028-0.01427.702-0.003-0.0030.0000.0000.0000.000
76B76LYS 11.0020.99432.232-0.049-0.0490.0000.0000.0000.000
77B77VAL 00.0240.00132.6720.0040.0040.0000.0000.0000.000
78B78GLY 00.0020.01132.097-0.005-0.0050.0000.0000.0000.000
79B79GLY 00.0020.02030.052-0.003-0.0030.0000.0000.0000.000
80B80SER 0-0.044-0.05124.8290.0060.0060.0000.0000.0000.000
81B81CYS 0-0.0130.02524.733-0.004-0.0040.0000.0000.0000.000
82B82VAL 00.0130.01218.2650.0040.0040.0000.0000.0000.000
83B83LEU 0-0.0090.00620.036-0.004-0.0040.0000.0000.0000.000
84B84SER 00.0490.02416.3620.0550.0550.0000.0000.0000.000
85B85GLY 00.0120.01614.497-0.054-0.0540.0000.0000.0000.000
86B86HIS 0-0.040-0.03014.7790.0190.0190.0000.0000.0000.000
87B87ASN 0-0.038-0.02912.5340.0930.0930.0000.0000.0000.000
88B88LEU 0-0.024-0.00512.630-0.012-0.0120.0000.0000.0000.000
89B89ALA 00.0300.01710.959-0.027-0.0270.0000.0000.0000.000
90B90LYS 10.9190.9939.576-0.741-0.7410.0000.0000.0000.000
91B91HIS 00.013-0.00611.430-0.025-0.0250.0000.0000.0000.000
92B92CYS 0-0.025-0.01115.084-0.018-0.0180.0000.0000.0000.000
93B93LEU 0-0.0300.00318.067-0.010-0.0100.0000.0000.0000.000
94B94HIS 00.0490.00720.613-0.035-0.0350.0000.0000.0000.000
95B95VAL 00.005-0.00223.788-0.007-0.0070.0000.0000.0000.000
96B96VAL 0-0.0280.01326.3660.0000.0000.0000.0000.0000.000
97B97GLY 00.0340.01830.066-0.007-0.0070.0000.0000.0000.000
98B98PRO 00.0020.01431.7470.0050.0050.0000.0000.0000.000
99B99ASN 0-0.0020.00334.687-0.004-0.0040.0000.0000.0000.000
100B100VAL 00.0840.04136.5320.0000.0000.0000.0000.0000.000
101B101ASN 0-0.045-0.01937.467-0.004-0.0040.0000.0000.0000.000
102B102LYS 10.7660.87936.337-0.049-0.0490.0000.0000.0000.000
103B103GLY 00.0060.01141.1200.0000.0000.0000.0000.0000.000
104B104GLU -1-0.820-0.86436.8830.0440.0440.0000.0000.0000.000
105B105ASP -1-0.820-0.91340.5950.0110.0110.0000.0000.0000.000
106B106ILE 00.0330.00136.5620.0020.0020.0000.0000.0000.000
107B107GLN 0-0.025-0.01337.4220.0010.0010.0000.0000.0000.000
108B108LEU 00.0200.00335.768-0.001-0.0010.0000.0000.0000.000
109B109LEU 0-0.034-0.01831.4790.0040.0040.0000.0000.0000.000
110B110LYS 10.8750.92931.8920.0170.0170.0000.0000.0000.000
111B111SER 00.0260.01431.459-0.001-0.0010.0000.0000.0000.000
112B112ALA 00.0270.00929.7940.0040.0040.0000.0000.0000.000
113B113TYR 00.022-0.01426.3590.0070.0070.0000.0000.0000.000
114B114GLU -1-0.876-0.91826.6350.0000.0000.0000.0000.0000.000
115B115ASN 0-0.023-0.00425.0050.0050.0050.0000.0000.0000.000
116B116PHE 00.027-0.01122.3010.0120.0120.0000.0000.0000.000
117B117ASN 0-0.044-0.01921.683-0.014-0.0140.0000.0000.0000.000
118B118GLN 0-0.0260.01222.176-0.010-0.0100.0000.0000.0000.000
119B119HIS 0-0.004-0.00417.2490.0290.0290.0000.0000.0000.000
120B120GLU -1-0.834-0.89815.599-0.123-0.1230.0000.0000.0000.000
121B121VAL 0-0.014-0.01012.807-0.041-0.0410.0000.0000.0000.000
122B122LEU 0-0.0110.02715.2460.0700.0700.0000.0000.0000.000
123B123LEU 0-0.0080.01314.807-0.042-0.0420.0000.0000.0000.000
124B124ALA 00.005-0.00917.1700.0340.0340.0000.0000.0000.000
125B125PRO 00.0020.01720.776-0.017-0.0170.0000.0000.0000.000
126B126LEU 00.0100.00523.919-0.002-0.0020.0000.0000.0000.000
127B127LEU 00.0160.01725.9170.0080.0080.0000.0000.0000.000
128B128SER 00.007-0.02728.823-0.008-0.0080.0000.0000.0000.000
129B129ALA 00.0200.02830.054-0.003-0.0030.0000.0000.0000.000
130B130GLY 00.0340.01531.7830.0070.0070.0000.0000.0000.000
131B131ILE 00.001-0.00431.411-0.003-0.0030.0000.0000.0000.000
132B132PHE 0-0.070-0.02530.7360.0000.0000.0000.0000.0000.000
133B133GLY 00.0250.01134.606-0.002-0.0020.0000.0000.0000.000
134B134ALA 0-0.019-0.00134.820-0.003-0.0030.0000.0000.0000.000
135B135ASP -1-0.813-0.91235.884-0.005-0.0050.0000.0000.0000.000
136B136PRO 0-0.032-0.02332.334-0.001-0.0010.0000.0000.0000.000
137B137ILE 00.008-0.00532.730-0.003-0.0030.0000.0000.0000.000
138B138HIS 00.0600.03334.666-0.006-0.0060.0000.0000.0000.000
139B139SER 0-0.022-0.02730.734-0.003-0.0030.0000.0000.0000.000
140B140LEU 0-0.024-0.01228.3940.0000.0000.0000.0000.0000.000
141B141ARG 10.8190.87630.8850.0350.0350.0000.0000.0000.000
142B142VAL 00.0270.01831.897-0.003-0.0030.0000.0000.0000.000
143B143CYS 0-0.0110.00826.5240.0000.0000.0000.0000.0000.000
144B144VAL 0-0.0110.00228.448-0.005-0.0050.0000.0000.0000.000
145B145ASP -1-0.764-0.83329.660-0.045-0.0450.0000.0000.0000.000
146B146THR 0-0.112-0.06129.2220.0020.0020.0000.0000.0000.000
147B147VAL 0-0.059-0.02023.4790.0020.0020.0000.0000.0000.000
148B148ARG 10.9190.96925.4610.0320.0320.0000.0000.0000.000
149B149THR 0-0.0130.01919.919-0.019-0.0190.0000.0000.0000.000
150B150ASN 0-0.045-0.01417.578-0.009-0.0090.0000.0000.0000.000
151B151VAL 00.0380.01718.4450.0220.0220.0000.0000.0000.000
152B152TYR 0-0.020-0.01016.634-0.028-0.0280.0000.0000.0000.000
153B153LEU 00.0240.00119.5130.0310.0310.0000.0000.0000.000
154B154ALA 0-0.002-0.00219.950-0.016-0.0160.0000.0000.0000.000
155B155VAL 0-0.027-0.01722.0380.0130.0130.0000.0000.0000.000
156B156PHE 00.0220.01224.651-0.009-0.0090.0000.0000.0000.000
157B157ASP -1-0.788-0.89126.179-0.002-0.0020.0000.0000.0000.000
158B158LYS 10.8660.91429.0190.0390.0390.0000.0000.0000.000
159B159ASN 0-0.009-0.02630.104-0.009-0.0090.0000.0000.0000.000
160B160LEU 0-0.0060.00530.612-0.003-0.0030.0000.0000.0000.000
161B161TYR 0-0.020-0.01925.542-0.003-0.0030.0000.0000.0000.000
162B162ASP -1-0.763-0.85629.929-0.047-0.0470.0000.0000.0000.000
163B163LYS 10.9451.01132.7570.0100.0100.0000.0000.0000.000
164B164LEU 0-0.0320.00629.525-0.001-0.0010.0000.0000.0000.000
165B165VAL 00.0320.00328.959-0.003-0.0030.0000.0000.0000.000
166B166SER 0-0.065-0.04031.859-0.002-0.0020.0000.0000.0000.000
167B167SER 0-0.020-0.02735.417-0.001-0.0010.0000.0000.0000.000
168B168PHE 0-0.0120.00431.3170.0020.0020.0000.0000.0000.000
169B169LEU -1-0.911-0.93134.175-0.056-0.0560.0000.0000.0000.000
170B212HOH 0-0.067-0.04711.8680.0410.0410.0000.0000.0000.000
171B219HOH 0-0.005-0.01233.7830.0010.0010.0000.0000.0000.000
172B224HOH 0-0.039-0.03138.8730.0010.0010.0000.0000.0000.000
173B228HOH 0-0.043-0.03327.7140.0000.0000.0000.0000.0000.000
174B233HOH 0-0.033-0.02911.549-0.025-0.0250.0000.0000.0000.000
175B244HOH 0-0.035-0.02931.1470.0020.0020.0000.0000.0000.000
176B249HOH 0-0.050-0.05133.9770.0020.0020.0000.0000.0000.000
177B251HOH 0-0.019-0.02122.8440.0040.0040.0000.0000.0000.000
178B252HOH 0-0.011-0.01328.521-0.004-0.0040.0000.0000.0000.000
179B255HOH 00.0160.00424.1040.0060.0060.0000.0000.0000.000
180B256HOH 0-0.025-0.03413.815-0.003-0.0030.0000.0000.0000.000
181B257HOH 0-0.010-0.03419.491-0.014-0.0140.0000.0000.0000.000
182B264HOH 0-0.041-0.03034.9070.0010.0010.0000.0000.0000.000
183B270HOH 0-0.022-0.00827.526-0.002-0.0020.0000.0000.0000.000
184B271HOH 00.0230.00129.596-0.002-0.0020.0000.0000.0000.000
185B273HOH 0-0.024-0.02328.4570.0010.0010.0000.0000.0000.000
186B274HOH 0-0.031-0.03023.1140.0060.0060.0000.0000.0000.000
187B276HOH 0-0.033-0.03022.9170.0010.0010.0000.0000.0000.000
188B279HOH 00.001-0.00322.2150.0030.0030.0000.0000.0000.000
189B281HOH 0-0.068-0.05129.128-0.003-0.0030.0000.0000.0000.000
190B282HOH 0-0.086-0.06237.083-0.001-0.0010.0000.0000.0000.000
191B285HOH 00.0220.01428.115-0.002-0.0020.0000.0000.0000.000
192B286HOH 0-0.019-0.03212.5750.0330.0330.0000.0000.0000.000
193B299HOH 0-0.016-0.01015.4070.0130.0130.0000.0000.0000.000
194B304HOH 00.009-0.01428.006-0.003-0.0030.0000.0000.0000.000
195B307HOH 0-0.040-0.03134.100-0.002-0.0020.0000.0000.0000.000
196B311HOH 00.0020.00331.7360.0030.0030.0000.0000.0000.000
197B314HOH 0-0.019-0.00229.5780.0030.0030.0000.0000.0000.000
198B317HOH 00.000-0.01434.7830.0020.0020.0000.0000.0000.000
199B321HOH 00.000-0.01715.8460.0190.0190.0000.0000.0000.000
200B322HOH 00.0350.02433.7760.0020.0020.0000.0000.0000.000
201B328HOH 00.0150.00528.415-0.003-0.0030.0000.0000.0000.000
202B331HOH 00.0170.00730.1430.0020.0020.0000.0000.0000.000
203B338HOH 00.006-0.00430.639-0.002-0.0020.0000.0000.0000.000
204B339HOH 00.0280.01831.8660.0010.0010.0000.0000.0000.000
205B349HOH 0-0.016-0.02728.7060.0000.0000.0000.0000.0000.000
206B356HOH 0-0.029-0.02028.9460.0000.0000.0000.0000.0000.000